Microbial compositions and methods for producing combined probiotic assemblages

Abstract

The present invention relates to the identification of a group of microorganisms, which are relatively abundant in the microbial communities associated with fruits and vegetables typically consumed raw and therefore transient or permanent members of the human microbiota. These microbes are used to augment the effects of additional probiotic strains. The consumption of mixtures of these microbes at relevant doses will produce a beneficial effect in the host mediated in part by production of short chain fatty acids to enhance colonic butyrate production. Therapeutic methods of the invention involve the use of live microorganisms or metabolites derived from said microorganisms to establish a microbial composition in the mammalian host that will provide a health benefit to a mammal in need thereof.

1 - 84 . (canceled) 
     
     
         85 . A composition comprising:
 A) at least one prebiotic compound, wherein the prebiotic compound comprises a prebiotic polysaccharide or a prebiotic fiber; and   B) a synthetic microbial consortium capable of a functional interaction, comprising:
 i) a first microbial entity comprising a yeast that encodes a gene or gene family capable of digesting the prebiotic compound; and 
 ii) a second microbial entity comprising at least two species selected from the group consisting of: a  Lactobacillus  sp., a  Leuconostoc  sp., a  Bacillus  sp., and combinations thereof, and 
   wherein the functional interaction comprises synergistic production of acetate relative to the capacity of each of the first microbial entity and the second microbial entity grown alone or the capacity of the two species of the second microbial entity in the absence of the first microbial entity.   
     
     
         86 . The composition of  claim 85 , wherein the gene or gene family capable of digesting the prebiotic compound is a glycosyl hydrolase (GH) selected from the group consisting of: GH81, GH76, GH63, GHS, GH47, GH37, GH18, GH17, GH16, GH15, GH132, and combination thereof. 
     
     
         87 . The composition of  claim 86 , wherein the second microbial entity does not encode the GH. 
     
     
         88 . The composition of  claim 85 , wherein the yeast is selected from the group consisting of: a  Saccharomyces  sp., a  Debaromyces  sp., a  Hanseniaspora  sp., and a  Pichia  sp. 
     
     
         89 . The composition of  claim 88 , wherein the  Pichia  sp. is  Pichia krudriavzevii.    
     
     
         90 . The composition of  claim 85 , wherein the second microbial entity comprises at least two entities selected from the group consisting of:  Lactobacillus reuteri, Lactobacillus paracasei, Lactobacillus salivarius Lactobacillus plantarum, Lactobacillus acidophilus, Lactobacillus reuteri protectis, Lactobacillus bulgaricus, Lactobacillus rhamnosus, Lactobacillus casei, Lactobacillus delbreukeii , and  Leuconostoc mesenteroides.    
     
     
         91 . The composition of  claim 85 , wherein the second microbial entity is a generally regarded as safe (GRAS) probiotic microorganism or a probiotic microorganism approved for human consumption. 
     
     
         92 . The composition of  claim 85 , wherein the second microbial entity comprises at least  Lactobacillus plantarum.    
     
     
         93 . The composition of  claim 85 , wherein the second microbial entity comprises at least  Lactobacillus brevis.    
     
     
         94 . The composition of  claim 85 , wherein the second microbial entity comprises at least  Leuconostoc mesenteroides.    
     
     
         95 . The probiotic composition of  claim 85 , wherein the prebiotic polysaccharide is oligofructose or fructooligosaccharide. 
     
     
         96 . The probiotic composition of  claim 85 , wherein the prebiotic polysaccharide comprises a plant or plant extract. 
     
     
         97 . The composition of  claim 85 , wherein no other cryoprotectant is present other than the prebiotic polysaccharide or the prebiotic fiber. 
     
     
         98 . The composition of  claim 85 , wherein the at least one prebiotic compound and the synthetic microbial consortium are co-formulated in a unit dosage form for oral administration to a subject. 
     
     
         99 . The composition of  claim 98 , wherein the unit dosage form comprises a medical food. 
     
     
         100 . The composition of  claim 85 , wherein the second microbial entity comprises at least each of a  Leuconostoc mesenteroides  species, a  Lactobacillus brevis  species, and a  Lactobacillus plantarum  species. 
     
     
         101 . The composition of  claim 85 , wherein the second microbial entity comprises each of (1) a  Leuconostoc mesenteroides  species having a 16s rRNA sequence at least 97% similarity to Seq ID NO: 157; (2) a  Lactobacillus brevis  species having a 16s rRNA sequence at least 97% similarity to Seq ID NO: 158; and (3) a  Lactobacillus plantarum  species having a 16s rRNA sequence at least 97% similarity to Seq ID NO: 163. 
     
     
         102 . A method for dietary management of bone health in a subject, the method comprising administering to the subject an effective amount of the composition of  claim 85 . 
     
     
         103 . A composition comprising:
 A) at least one prebiotic compound, wherein the prebiotic compound comprises a prebiotic polysaccharide or a prebiotic fiber; and   B) a synthetic microbial consortium, comprising:
 i) a first microbial entity comprising a yeast that encodes a gene or gene family capable of digesting the prebiotic compound; and 
 ii) a second microbial entity comprising at least two species selected from the group consisting of: a  Lactobacillus  sp., a  Leuconostoc  sp., a  Bacillus  sp., and combinations thereof, 
   wherein the gene or gene family capable of digesting the prebiotic compound is a glycosyl hydrolase (GH) selected from the group consisting of: GH81, GH76, GH63, GHS, GH47, GH37, GH18, GH17, GH16, GH15, GH132, and combination thereof, and wherein the second microbial entity does not encode the GH.